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- PDB-1a0r: HETEROTRIMERIC COMPLEX OF PHOSDUCIN/TRANSDUCIN BETA-GAMMA -

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Basic information

Entry
Database: PDB / ID: 1a0r
TitleHETEROTRIMERIC COMPLEX OF PHOSDUCIN/TRANSDUCIN BETA-GAMMA
Components
  • PHOSDUCIN
  • TRANSDUCIN (BETA SUBUNIT)
  • TRANSDUCIN (GAMMA SUBUNIT)
KeywordsCOMPLEX (TRANSDUCER/TRANSDUCTION) / PHOSDUCIN / TRANSDUCIN / BETA-GAMMA / SIGNAL TRANSDUCTION / REGULATION / PHOSPHORYLATION / G PROTEINS / THIOREDOXIN / VISION / MEKA / COMPLEX (TRANSDUCER-TRANSDUCTION) / POST-TRANSLATIONAL MODIFICATION / FARNESYL / FARNESYLATION / COMPLEX (TRANSDUCER-TRANSDUCTION) complex
Function / homology
Function and homology information


Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / regulation of G protein-coupled receptor signaling pathway / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / regulation of G protein-coupled receptor signaling pathway / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / phototransduction / photoreceptor outer segment / photoreceptor inner segment / visual perception / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / intracellular protein localization / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / cell population proliferation / G protein-coupled receptor signaling pathway / GTPase activity / synapse / protein-containing complex binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Phosducin, domain 2 / Phosducin; domain 2 / Phosducin / Phosducin, N-terminal domain superfamily / : / Phosducin, thioredoxin-like domain / Phosducin / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase ...Phosducin, domain 2 / Phosducin; domain 2 / Phosducin / Phosducin, N-terminal domain superfamily / : / Phosducin, thioredoxin-like domain / Phosducin / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Glutaredoxin / Glutaredoxin / Few Secondary Structures / Irregular / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / WD domain, G-beta repeat / Thioredoxin-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FARNESYL / Guanine nucleotide-binding protein G(T) subunit gamma-T1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Phosducin / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, CROSS-CRYSTAL A / Resolution: 2.8 Å
AuthorsLoew, A. / Ho, Y.-K. / Blundell, T.L. / Bax, B.
Citation
Journal: Structure / Year: 1998
Title: Phosducin induces a structural change in transducin beta gamma.
Authors: Loew, A. / Ho, Y.K. / Blundell, T. / Bax, B.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal Structure at 2.4 Angstroms Resolution of the Complex of Transducin Betagamma and its Regulator, Phosducin
Authors: Gaudet, R. / Bohm, A. / Sigler, P.B.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: The Structure of the G Protein Heterotrimer Gi Alpha 1 Beta 1 Gamma 2
Authors: Wall, M.A. / Coleman, D.E. / Lee, E. / Iniguez-Lluhi, J.A. / Posner, B.A. / Gilman, A.G. / Sprang, S.R.
History
DepositionDec 5, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status / pdbx_validate_polymer_linkage
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Jun 24, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.6Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.8Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: TRANSDUCIN (BETA SUBUNIT)
G: TRANSDUCIN (GAMMA SUBUNIT)
P: PHOSDUCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4684
Polymers73,2613
Non-polymers2061
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-55 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.090, 87.910, 98.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRANSDUCIN (BETA SUBUNIT) / GT BETA


Mass: 37325.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFIED FROM BOVINE ROD OUTER SEGMENT / Source: (natural) Bos taurus (domestic cattle) / Cellular location: ROD OUTER SEGMENTS / Organ: EYE / Tissue: RETINA / References: UniProt: P04901, UniProt: P62871*PLUS
#2: Protein TRANSDUCIN (GAMMA SUBUNIT) / GT GAMMA


Mass: 7666.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFIED FROM BOVINE ROD OUTER SEGMENT / Source: (natural) Bos taurus (domestic cattle) / Cellular location: ROD OUTER SEGMENTS / Organ: EYE / Tissue: RETINA / References: UniProt: P02698
#3: Protein PHOSDUCIN / MEKA / PP33


Mass: 28268.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PURIFIED FROM BOVINE ROD OUTER SEGMENT IN COMPLEX WITH TRANSDUCIN BETA-GAMMA SUBUNIT
Source: (natural) Bos taurus (domestic cattle) / Cellular location: ROD OUTER SEGMENTS / Organ: EYE / Tissue: RETINA / References: UniProt: P19632
#4: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.8
Details: THE PROTEIN COMPLEX (10 MG/ML SOLUTION) WAS CRYSTALLIZED FROM 400 MM SODIUM CACODYLATE (PH 6.8), 1 MM ZINC CHLORIDE, 25 % ETHYLENE GLYCOL, 12 % PEG 8000, BY MICROBATCH CRYSTALLIZATION AT 4 ...Details: THE PROTEIN COMPLEX (10 MG/ML SOLUTION) WAS CRYSTALLIZED FROM 400 MM SODIUM CACODYLATE (PH 6.8), 1 MM ZINC CHLORIDE, 25 % ETHYLENE GLYCOL, 12 % PEG 8000, BY MICROBATCH CRYSTALLIZATION AT 4 DEGREES C., microbatch, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
2400 mMcacodylic acid/NaOH11
31 mM11ZnCl2
41 mMbeta-mercaptoethanol11
51 mMPMSF11
61 mMbenzamidine11
725 %ethylene glycol11
812 %PEG800011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9194
DetectorDetector: CCD / Date: Apr 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 15784 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 3.09 % / Biso Wilson estimate: 31.6 Å2 / Rsym value: 0.08
Reflection shellResolution: 2.8→2.9 Å / Rsym value: 0.315 / % possible all: 97.8
Reflection
*PLUS
Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.315

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: molecular replacement, CROSS-CRYSTAL A
Starting model: BETA-GAMMA CHAIN OF 1GP2

1gp2


Resolution: 2.8→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 909 7.6 %SHELLS
Rwork0.228 ---
obs0.228 11938 71 %-
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4659 0 18 21 4698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.94
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.271.5
X-RAY DIFFRACTIONx_mcangle_it2.22
X-RAY DIFFRACTIONx_scbond_it1.712
X-RAY DIFFRACTIONx_scangle_it2.672.5
LS refinement shellResolution: 2.8→2.93 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.379 65 6.8 %
Rwork0.296 889 -
obs--45.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_ACE.PROTOPHCSDX_NEW.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3FAR.PARFAR.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.222 / Rfactor Rfree: 0.261
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor obs: 0.296

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